1 LIN5/6 comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 LIN5/6 model characteristics

The main characteristics of the Test Case LIN5/6 (ling) CASAL model are:

  • one stock, ages 3 - 25
  • one area
  • years 1972 - 2018, projection years 2019 - 2023
  • two time steps: Dec_Aug and Sep_Nov
  • two stock categories: male and female
  • natural mortality-at-age is double exponential
  • sex-specific maturity ogives specified by age
  • sex-specific age-length von Bertalanffy relationship
  • sex-specific length-weight relationship
  • Beverton-Holt stock-recruitment relationship, with steepness (h) set to 0.84
  • ageing error
  • two surveys with sex-specific logistic selectivity
  • three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

  • survey indices
  • survey proportions-at-age
  • fishery proportions-at-age

Parameters estimated include:

  • B0
  • parameters for the natural mortality-at-age ogive
  • free catchability (q) for the two surveys
  • parameters for the sex-specific selectivity curves for the two surveys
  • parameters for the sex-specific selectivity curves for the three fisheries
  • year-class strengths (recruitment deviations)

1.2 R environment

## [1] "Thu May 28 17:13:22 2020"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux bullseye/sid
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] casal2_1.0     casal_2.30     devtools_2.3.0 usethis_1.6.1  rlist_0.4.6.1 
## [6] ggplot2_3.3.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6      pillar_1.4.4      compiler_3.6.3    remotes_2.1.1    
##  [5] prettyunits_1.1.1 tools_3.6.3       testthat_2.3.2    pkgload_1.0.2    
##  [9] pkgbuild_1.0.8    digest_0.6.25     memoise_1.1.0     evaluate_0.14    
## [13] lifecycle_0.2.0   tibble_3.0.1      gtable_0.3.0      pkgconfig_2.0.3  
## [17] rlang_0.4.6       cli_2.0.2         yaml_2.2.1        xfun_0.14        
## [21] withr_2.2.0       stringr_1.4.0     dplyr_0.8.5       knitr_1.28       
## [25] desc_1.2.0        vctrs_0.3.0       fs_1.4.1          rprojroot_1.3-2  
## [29] grid_3.6.3        tidyselect_1.1.0  glue_1.4.1        data.table_1.12.8
## [33] R6_2.4.1          processx_3.4.2    fansi_0.4.1       rmarkdown_2.1    
## [37] sessioninfo_1.1.1 callr_3.4.3       purrr_0.3.4       magrittr_1.5     
## [41] backports_1.1.7   ps_1.3.3          scales_1.1.1      ellipsis_0.3.1   
## [45] htmltools_0.4.0   assertthat_0.2.1  colorspace_1.4-1  stringi_1.4.6    
## [49] munsell_0.5.0     crayon_1.3.4

1.3 CASAL and Casal2 model output

# read in CASAL MPD results
cas_mpd_filename <- file.path(base_dir, 'CASAL', mpd_run)
cas_mpd  <- casal::extract.mpd(cas_mpd_filename)
cas_corr <- casal::extract.correlation.matrix(cas_mpd_filename)
cas_conv <- get_convergence_information(cas_mpd_filename)
c1_quant <- cas_mpd$quantities

cas_mpd_sens1_filename <- file.path(base_dir, 'CASAL_sens1', mpd_run)
cas_mpd_sens1  <- casal::extract.mpd(cas_mpd_sens1_filename)
cas_sens1_corr <- casal::extract.correlation.matrix(cas_mpd_sens1_filename)
cas_sens1_conv <- get_convergence_information(cas_mpd_sens1_filename)
c1_sens1_quant <- cas_mpd_sens1$quantities
C2_subdir <- c('betadiff_casal_flags_on',
               'betadiff_casal_flags_off',
               'betadiff_casal_flags_on_low_tol',
               'cppad_casal_flags_on',
               'cppad_casal_flags_off',
               'adolc_casal_flags_on',
               'adolc_casal_flags_off',
               'adolc_casal_flags_on_low_tol')


# find the non-zero-sized parameter estimate files for the C2 models
C2_subdir <- unlist(sapply(C2_subdir, function(c_dir) if ( file.access(file.path(base_dir, 'Casal2', c_dir, params_est), 4) == 0 &
                                                           file.size(file.path(base_dir, 'Casal2', c_dir, params_est)) > 0 )
                                                         { return (c_dir) }, USE.NAMES=FALSE ))


num_C2_models <- length(C2_subdir)

C2_color <- c('blue', 'green3', 'red', 'gold', 'magenta', 'cyan', 'brown', 'orange')

# read in Casal2 MPD results
cas2_mpd  <- list()
cas2_corr <- list()
cas2_conv <- list()
for (c in 1:num_C2_models)
{
    cas2_mpd_filename <- file.path(base_dir, 'Casal2', C2_subdir[c], mpd_run)
    cas2_mpd[[c]] <- casal2::extract.mpd(cas2_mpd_filename)

    cas2_corr[[c]] <- casal2::extract.correlation.matrix(mpd_out, file.path(base_dir, 'Casal2', C2_subdir[c]))

    cas2_conv[[c]] <- get_convergence_information(cas2_mpd_filename)
}

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates and Percent Difference
rownames Base_Model Sensitivity_1 Percent_Diff
q[tan_sum].q          0.09128 0.09105 0.251
q[tan_aut].q          0.12625 0.12592 0.258
initialization.B0         308952.00000 310671.00000 -0.556
natural_mortality.ogive_all1 12.49210 12.98210 -3.922
natural_mortality.ogive_all2 0.13271 0.12782 3.680
natural_mortality.ogive_all3 0.38192 0.44986 -17.790
natural_mortality.ogive_all4 0.35058 0.35395 -0.960
selectivity[surveysum_sel].male1      4.73847 4.88131 -3.014
selectivity[surveysum_sel].male2      1.74997 1.77236 -1.279
selectivity[surveysum_sel].male3      0.61001 0.60162 1.375
selectivity[surveysum_sel].female1    5.46022 5.61310 -2.800
selectivity[surveysum_sel].female2    2.20584 2.21537 -0.432
selectivity[surveyaut_sel].male1      5.50416 5.64383 -2.538
selectivity[surveyaut_sel].male2      2.31427 2.29812 0.698
selectivity[surveyaut_sel].male3      0.93922 0.93314 0.648
selectivity[surveyaut_sel].female1    5.92021 6.06245 -2.403
selectivity[surveyaut_sel].female2    2.77781 2.73777 1.441
selectivity[trawl_sel].male1      8.36987 8.40438 -0.412
selectivity[trawl_sel].male2      1.97182 1.94699 1.259
selectivity[trawl_sel].male3      61.64930 200.00000 -224.416
selectivity[trawl_sel].male4      1.04125 1.02062 1.981
selectivity[trawl_sel].female1    8.66384 8.74135 -0.895
selectivity[trawl_sel].female2    2.09989 2.08792 0.570
selectivity[trawl_sel].female3    43.31110 40.38180 6.763
selectivity[line_home_sel].male1      11.45120 8.58352 25.043
selectivity[line_home_sel].male2      8.59023 4.54774 47.059
selectivity[line_home_sel].male3      0.38005 0.26910 29.193
selectivity[line_home_sel].female1    9.61555 9.53091 0.880
selectivity[line_home_sel].female2    3.87496 3.68517 4.898
selectivity[line_spawn_sel].male1      18.29980 14.03630 23.298
selectivity[line_spawn_sel].male2      13.66550 10.01380 26.722
selectivity[line_spawn_sel].male3      1.86791 1.17322 37.191
selectivity[line_spawn_sel].female1    9.74583 9.71344 0.332
selectivity[line_spawn_sel].female2    3.00787 2.89355 3.801
recruitment.YCS1       1.00000 1.00000 0.000
recruitment.YCS2       1.00000 1.00000 0.000
recruitment.YCS3       1.00000 1.00000 0.000
recruitment.YCS4       1.00000 1.00000 0.000
recruitment.YCS5       0.48497 0.46622 3.866
recruitment.YCS6       0.45827 0.45012 1.779
recruitment.YCS7       0.56856 0.56472 0.676
recruitment.YCS8       0.56672 0.56673 -0.001
recruitment.YCS9       0.48607 0.49069 -0.950
recruitment.YCS10      0.55503 0.56723 -2.198
recruitment.YCS11      0.56325 0.57884 -2.767
recruitment.YCS12      0.68756 0.71085 -3.387
recruitment.YCS13      0.62029 0.63612 -2.551
recruitment.YCS14      0.79057 0.80842 -2.257
recruitment.YCS15      0.46428 0.46926 -1.073
recruitment.YCS16      0.70075 0.70727 -0.929
recruitment.YCS17      0.41010 0.41046 -0.087
recruitment.YCS18      0.51501 0.51452 0.096
recruitment.YCS19      0.34165 0.34217 -0.154
recruitment.YCS20      0.34829 0.34726 0.295
recruitment.YCS21      0.43607 0.43820 -0.487
recruitment.YCS22      0.48058 0.47500 1.162
recruitment.YCS23      0.45216 0.45129 0.192
recruitment.YCS24      0.49168 0.49479 -0.631
recruitment.YCS25      0.46910 0.47066 -0.334
recruitment.YCS26      0.79927 0.80495 -0.710
recruitment.YCS27      0.79012 0.79211 -0.251
recruitment.YCS28      0.82606 0.83114 -0.615
recruitment.YCS29      0.70756 0.71251 -0.699
recruitment.YCS30      0.55170 0.55428 -0.468
recruitment.YCS31      0.47520 0.47677 -0.331
recruitment.YCS32      0.46170 0.46138 0.070
recruitment.YCS33      0.55496 0.55435 0.110
recruitment.YCS34      0.54666 0.54206 0.841
recruitment.YCS35      0.48323 0.48254 0.143
recruitment.YCS36      0.55016 0.54989 0.049
recruitment.YCS37      0.61527 0.61581 -0.087
recruitment.YCS38      0.77573 0.77473 0.129
recruitment.YCS39      0.63109 0.63059 0.080
recruitment.YCS40      0.77552 0.77349 0.262
recruitment.YCS41      0.64292 0.63935 0.555
recruitment.YCS42      0.70666 0.69938 1.030
recruitment.YCS43      0.65426 0.64860 0.864
recruitment.YCS44      0.50999 0.50618 0.746
recruitment.YCS45      0.58619 0.58729 -0.186
recruitment.YCS46      0.60348 0.58927 2.355
recruitment.YCS47      0.57681 0.57449 0.403
Casal2 parameter estimates
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
process[Recruitment].b0               308529.000 308529.000 310577.000 310576.000 310576.000 308529.000 308529.000 310577.000
catchability[summerTANq].q                0.091 0.091 0.091 0.091 0.091 0.091 0.091 0.091
catchability[autumnTANq].q                0.126 0.126 0.126 0.126 0.126 0.126 0.126 0.126
selectivity[M_all].x0               12.496 12.496 12.984 12.984 12.984 12.496 12.496 12.984
selectivity[M_all].y0               0.133 0.133 0.128 0.128 0.128 0.133 0.133 0.128
selectivity[M_all].y1               0.383 0.383 0.447 0.447 0.447 0.383 0.383 0.447
selectivity[M_all].y2               0.351 0.351 0.354 0.354 0.354 0.351 0.351 0.354
selectivity[summerTANSel_m].a50              4.740 4.740 4.876 4.876 4.876 4.740 4.740 4.876
selectivity[summerTANSel_m].ato95            1.745 1.745 1.770 1.770 1.770 1.745 1.745 1.770
selectivity[summerTANSel_m].alpha            0.610 0.610 0.602 0.602 0.602 0.610 0.610 0.602
selectivity[summerTANSel_f].a50              5.461 5.461 5.608 5.608 5.608 5.461 5.461 5.608
selectivity[summerTANSel_f].ato95            2.203 2.203 2.214 2.214 2.214 2.203 2.203 2.214
selectivity[autumnTANSel_m].a50              5.510 5.510 5.640 5.640 5.640 5.510 5.510 5.640
selectivity[autumnTANSel_m].ato95            2.313 2.313 2.298 2.298 2.298 2.313 2.313 2.298
selectivity[autumnTANSel_m].alpha            0.942 0.942 0.933 0.933 0.933 0.942 0.942 0.933
selectivity[autumnTANSel_f].a50              5.916 5.916 6.058 6.058 6.058 5.916 5.916 6.058
selectivity[autumnTANSel_f].ato95            2.770 2.770 2.738 2.738 2.738 2.770 2.770 2.738
selectivity[trwlFSel_m].mu               8.369 8.369 8.402 8.402 8.402 8.369 8.369 8.402
selectivity[trwlFSel_m].sigma_l          1.970 1.970 1.947 1.947 1.947 1.970 1.970 1.947
selectivity[trwlFSel_m].sigma_r          61.523 61.523 200.000 200.000 200.000 61.523 61.523 200.000
selectivity[trwlFSel_m].alpha            1.043 1.043 1.021 1.021 1.021 1.043 1.043 1.021
selectivity[trwlFSel_f].mu               8.659 8.659 8.739 8.739 8.739 8.659 8.659 8.739
selectivity[trwlFSel_f].sigma_l          2.097 2.097 2.088 2.088 2.088 2.097 2.097 2.088
selectivity[trwlFSel_f].sigma_r          43.164 43.164 40.595 40.594 40.594 43.164 43.164 40.595
selectivity[lineHomeFSel_m].a50              11.456 11.456 8.608 8.608 8.608 11.456 11.456 8.608
selectivity[lineHomeFSel_m].ato95            8.600 8.600 4.592 4.592 4.592 8.600 8.600 4.592
selectivity[lineHomeFSel_m].alpha            0.380 0.380 0.270 0.270 0.270 0.380 0.380 0.270
selectivity[lineHomeFSel_f].a50              9.615 9.615 9.534 9.534 9.534 9.615 9.615 9.534
selectivity[lineHomeFSel_f].ato95            3.870 3.870 3.691 3.691 3.691 3.870 3.870 3.691
selectivity[lineSpawnFSel_m].a50              18.215 18.215 14.047 14.047 14.047 18.215 18.215 14.047
selectivity[lineSpawnFSel_m].ato95            13.600 13.600 10.026 10.026 10.026 13.600 13.600 10.026
selectivity[lineSpawnFSel_m].alpha            1.856 1.856 1.174 1.174 1.174 1.856 1.856 1.174
selectivity[lineSpawnFSel_f].a50              9.739 9.739 9.715 9.715 9.715 9.739 9.739 9.715
selectivity[lineSpawnFSel_f].ato95            2.994 2.994 2.897 2.897 2.897 2.994 2.994 2.897
process[Recruitment].ycs_values{1972} 0.484 0.484 0.466 0.466 0.466 0.484 0.484 0.466
process[Recruitment].ycs_values{1973} 0.461 0.461 0.450 0.450 0.450 0.461 0.461 0.450
process[Recruitment].ycs_values{1974} 0.568 0.568 0.565 0.565 0.565 0.568 0.568 0.565
process[Recruitment].ycs_values{1975} 0.567 0.567 0.567 0.567 0.567 0.567 0.567 0.567
process[Recruitment].ycs_values{1976} 0.486 0.486 0.491 0.491 0.491 0.486 0.486 0.491
process[Recruitment].ycs_values{1977} 0.554 0.554 0.567 0.567 0.567 0.554 0.554 0.567
process[Recruitment].ycs_values{1978} 0.563 0.563 0.579 0.579 0.579 0.563 0.563 0.579
process[Recruitment].ycs_values{1979} 0.689 0.689 0.711 0.711 0.711 0.689 0.689 0.711
process[Recruitment].ycs_values{1980} 0.621 0.621 0.636 0.636 0.636 0.621 0.621 0.636
process[Recruitment].ycs_values{1981} 0.792 0.792 0.808 0.808 0.808 0.792 0.792 0.808
process[Recruitment].ycs_values{1982} 0.465 0.465 0.469 0.469 0.469 0.465 0.465 0.469
process[Recruitment].ycs_values{1983} 0.700 0.700 0.707 0.707 0.707 0.700 0.700 0.707
process[Recruitment].ycs_values{1984} 0.410 0.410 0.410 0.410 0.410 0.410 0.410 0.410
process[Recruitment].ycs_values{1985} 0.515 0.515 0.515 0.515 0.515 0.515 0.515 0.515
process[Recruitment].ycs_values{1986} 0.341 0.341 0.342 0.342 0.342 0.341 0.341 0.342
process[Recruitment].ycs_values{1987} 0.348 0.348 0.347 0.347 0.347 0.348 0.348 0.347
process[Recruitment].ycs_values{1988} 0.438 0.438 0.438 0.438 0.438 0.438 0.438 0.438
process[Recruitment].ycs_values{1989} 0.479 0.479 0.475 0.475 0.475 0.479 0.479 0.475
process[Recruitment].ycs_values{1990} 0.452 0.452 0.451 0.451 0.451 0.452 0.452 0.451
process[Recruitment].ycs_values{1991} 0.493 0.493 0.495 0.495 0.495 0.493 0.493 0.495
process[Recruitment].ycs_values{1992} 0.469 0.469 0.471 0.471 0.471 0.469 0.469 0.471
process[Recruitment].ycs_values{1993} 0.798 0.798 0.805 0.805 0.805 0.798 0.798 0.805
process[Recruitment].ycs_values{1994} 0.791 0.791 0.792 0.792 0.792 0.791 0.791 0.792
process[Recruitment].ycs_values{1995} 0.825 0.825 0.831 0.831 0.831 0.825 0.825 0.831
process[Recruitment].ycs_values{1996} 0.707 0.707 0.712 0.712 0.712 0.707 0.707 0.712
process[Recruitment].ycs_values{1997} 0.552 0.552 0.554 0.554 0.554 0.552 0.552 0.554
process[Recruitment].ycs_values{1998} 0.475 0.475 0.477 0.477 0.477 0.475 0.475 0.477
process[Recruitment].ycs_values{1999} 0.461 0.461 0.461 0.461 0.461 0.461 0.461 0.461
process[Recruitment].ycs_values{2000} 0.556 0.556 0.554 0.554 0.554 0.556 0.556 0.554
process[Recruitment].ycs_values{2001} 0.545 0.545 0.542 0.542 0.542 0.545 0.545 0.542
process[Recruitment].ycs_values{2002} 0.484 0.484 0.483 0.483 0.483 0.484 0.484 0.483
process[Recruitment].ycs_values{2003} 0.550 0.550 0.550 0.550 0.550 0.550 0.550 0.550
process[Recruitment].ycs_values{2004} 0.614 0.614 0.616 0.616 0.616 0.614 0.614 0.616
process[Recruitment].ycs_values{2005} 0.777 0.777 0.775 0.775 0.775 0.777 0.777 0.775
process[Recruitment].ycs_values{2006} 0.631 0.631 0.631 0.631 0.631 0.631 0.631 0.631
process[Recruitment].ycs_values{2007} 0.774 0.774 0.773 0.773 0.773 0.774 0.774 0.773
process[Recruitment].ycs_values{2008} 0.643 0.643 0.639 0.639 0.639 0.643 0.643 0.639
process[Recruitment].ycs_values{2009} 0.706 0.706 0.699 0.699 0.699 0.706 0.706 0.699
process[Recruitment].ycs_values{2010} 0.653 0.653 0.649 0.649 0.649 0.653 0.653 0.649
process[Recruitment].ycs_values{2011} 0.511 0.511 0.506 0.506 0.506 0.511 0.511 0.506
process[Recruitment].ycs_values{2012} 0.586 0.586 0.587 0.587 0.587 0.586 0.586 0.587
process[Recruitment].ycs_values{2013} 0.601 0.601 0.589 0.589 0.589 0.601 0.601 0.589
process[Recruitment].ycs_values{2014} 0.576 0.576 0.574 0.574 0.574 0.576 0.576 0.574
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
process[Recruitment].b0               0.000 0.000 -0.664 -0.663 -0.663 0.000 0.000 -0.664
catchability[summerTANq].q                0.000 0.000 0.344 0.344 0.344 0.000 0.000 0.344
catchability[autumnTANq].q                0.000 0.000 0.105 0.105 0.105 0.000 0.000 0.105
selectivity[M_all].x0               0.000 0.000 -3.904 -3.904 -3.904 0.000 0.000 -3.904
selectivity[M_all].y0               0.000 0.000 3.510 3.510 3.510 0.000 0.000 3.510
selectivity[M_all].y1               0.000 0.000 -16.840 -16.841 -16.841 0.000 0.000 -16.840
selectivity[M_all].y2               0.000 0.000 -0.741 -0.740 -0.740 0.000 0.000 -0.741
selectivity[summerTANSel_m].a50              0.000 0.000 -2.881 -2.882 -2.882 0.000 0.000 -2.881
selectivity[summerTANSel_m].ato95            0.000 0.000 -1.473 -1.473 -1.473 0.000 0.000 -1.473
selectivity[summerTANSel_m].alpha            0.000 0.000 1.329 1.329 1.329 0.000 0.000 1.329
selectivity[summerTANSel_f].a50              0.000 0.000 -2.691 -2.691 -2.691 0.000 0.000 -2.691
selectivity[summerTANSel_f].ato95            0.000 0.000 -0.490 -0.490 -0.490 0.000 0.000 -0.490
selectivity[autumnTANSel_m].a50              0.000 0.000 -2.358 -2.358 -2.358 0.000 0.000 -2.358
selectivity[autumnTANSel_m].ato95            0.000 0.000 0.644 0.644 0.644 0.000 0.000 0.644
selectivity[autumnTANSel_m].alpha            0.000 0.000 0.906 0.907 0.907 0.000 0.000 0.906
selectivity[autumnTANSel_f].a50              0.000 0.000 -2.413 -2.413 -2.413 0.000 0.000 -2.413
selectivity[autumnTANSel_f].ato95            0.000 0.000 1.146 1.146 1.146 0.000 0.000 1.146
selectivity[trwlFSel_m].mu               0.000 0.000 -0.397 -0.397 -0.397 0.000 0.000 -0.397
selectivity[trwlFSel_m].sigma_l          0.000 0.000 1.161 1.161 1.161 0.000 0.000 1.161
selectivity[trwlFSel_m].sigma_r          0.000 0.000 -225.082 -225.082 -225.082 0.000 0.000 -225.082
selectivity[trwlFSel_m].alpha            0.000 0.000 2.101 2.101 2.101 0.000 0.000 2.101
selectivity[trwlFSel_f].mu               0.000 0.000 -0.935 -0.935 -0.935 0.000 0.000 -0.935
selectivity[trwlFSel_f].sigma_l          0.000 0.000 0.385 0.385 0.385 0.000 0.000 0.385
selectivity[trwlFSel_f].sigma_r          0.000 0.000 5.952 5.954 5.954 0.000 0.000 5.952
selectivity[lineHomeFSel_m].a50              0.000 0.000 24.857 24.858 24.858 0.000 0.000 24.857
selectivity[lineHomeFSel_m].ato95            0.000 0.000 46.606 46.607 46.607 0.000 0.000 46.606
selectivity[lineHomeFSel_m].alpha            0.000 0.000 29.007 29.008 29.008 0.000 0.000 29.007
selectivity[lineHomeFSel_f].a50              0.000 0.000 0.845 0.845 0.845 0.000 0.000 0.845
selectivity[lineHomeFSel_f].ato95            0.000 0.000 4.638 4.638 4.638 0.000 0.000 4.638
selectivity[lineSpawnFSel_m].a50              0.000 0.000 22.884 22.884 22.884 0.000 0.000 22.884
selectivity[lineSpawnFSel_m].ato95            0.000 0.000 26.276 26.277 26.277 0.000 0.000 26.276
selectivity[lineSpawnFSel_m].alpha            0.000 0.000 36.731 36.731 36.731 0.000 0.000 36.731
selectivity[lineSpawnFSel_f].a50              0.000 0.000 0.245 0.245 0.245 0.000 0.000 0.245
selectivity[lineSpawnFSel_f].ato95            0.000 0.000 3.246 3.246 3.246 0.000 0.000 3.246
process[Recruitment].ycs_values{1972} 0.000 0.000 3.589 3.589 3.589 0.000 0.000 3.589
process[Recruitment].ycs_values{1973} 0.000 0.000 2.389 2.389 2.389 0.000 0.000 2.389
process[Recruitment].ycs_values{1974} 0.000 0.000 0.675 0.675 0.675 0.000 0.000 0.675
process[Recruitment].ycs_values{1975} 0.000 0.000 -0.064 -0.064 -0.064 0.000 0.000 -0.064
process[Recruitment].ycs_values{1976} 0.000 0.000 -0.916 -0.916 -0.916 0.000 0.000 -0.916
process[Recruitment].ycs_values{1977} 0.000 0.000 -2.353 -2.353 -2.353 0.000 0.000 -2.353
process[Recruitment].ycs_values{1978} 0.000 0.000 -2.733 -2.732 -2.732 0.000 0.000 -2.733
process[Recruitment].ycs_values{1979} 0.000 0.000 -3.185 -3.185 -3.185 0.000 0.000 -3.185
process[Recruitment].ycs_values{1980} 0.000 0.000 -2.457 -2.457 -2.457 0.000 0.000 -2.457
process[Recruitment].ycs_values{1981} 0.000 0.000 -1.962 -1.962 -1.962 0.000 0.000 -1.962
process[Recruitment].ycs_values{1982} 0.000 0.000 -0.906 -0.906 -0.906 0.000 0.000 -0.906
process[Recruitment].ycs_values{1983} 0.000 0.000 -1.056 -1.056 -1.056 0.000 0.000 -1.056
process[Recruitment].ycs_values{1984} 0.000 0.000 -0.115 -0.115 -0.115 0.000 0.000 -0.115
process[Recruitment].ycs_values{1985} 0.000 0.000 0.162 0.162 0.162 0.000 0.000 0.162
process[Recruitment].ycs_values{1986} 0.000 0.000 -0.236 -0.235 -0.235 0.000 0.000 -0.236
process[Recruitment].ycs_values{1987} 0.000 0.000 0.091 0.091 0.091 0.000 0.000 0.091
process[Recruitment].ycs_values{1988} 0.000 0.000 -0.079 -0.078 -0.078 0.000 0.000 -0.079
process[Recruitment].ycs_values{1989} 0.000 0.000 0.884 0.885 0.885 0.000 0.000 0.884
process[Recruitment].ycs_values{1990} 0.000 0.000 0.106 0.106 0.106 0.000 0.000 0.106
process[Recruitment].ycs_values{1991} 0.000 0.000 -0.436 -0.436 -0.436 0.000 0.000 -0.436
process[Recruitment].ycs_values{1992} 0.000 0.000 -0.325 -0.325 -0.325 0.000 0.000 -0.325
process[Recruitment].ycs_values{1993} 0.000 0.000 -0.871 -0.871 -0.871 0.000 0.000 -0.871
process[Recruitment].ycs_values{1994} 0.000 0.000 -0.102 -0.102 -0.102 0.000 0.000 -0.102
process[Recruitment].ycs_values{1995} 0.000 0.000 -0.691 -0.691 -0.691 0.000 0.000 -0.691
process[Recruitment].ycs_values{1996} 0.000 0.000 -0.736 -0.736 -0.736 0.000 0.000 -0.736
process[Recruitment].ycs_values{1997} 0.000 0.000 -0.400 -0.400 -0.400 0.000 0.000 -0.400
process[Recruitment].ycs_values{1998} 0.000 0.000 -0.368 -0.368 -0.368 0.000 0.000 -0.368
process[Recruitment].ycs_values{1999} 0.000 0.000 -0.045 -0.045 -0.045 0.000 0.000 -0.045
process[Recruitment].ycs_values{2000} 0.000 0.000 0.239 0.239 0.239 0.000 0.000 0.239
process[Recruitment].ycs_values{2001} 0.000 0.000 0.623 0.623 0.623 0.000 0.000 0.623
process[Recruitment].ycs_values{2002} 0.000 0.000 0.227 0.227 0.227 0.000 0.000 0.227
process[Recruitment].ycs_values{2003} 0.000 0.000 -0.008 -0.007 -0.007 0.000 0.000 -0.008
process[Recruitment].ycs_values{2004} 0.000 0.000 -0.260 -0.260 -0.260 0.000 0.000 -0.260
process[Recruitment].ycs_values{2005} 0.000 0.000 0.321 0.321 0.321 0.000 0.000 0.321
process[Recruitment].ycs_values{2006} 0.000 0.000 0.123 0.124 0.124 0.000 0.000 0.123
process[Recruitment].ycs_values{2007} 0.000 0.000 0.042 0.042 0.042 0.000 0.000 0.042
process[Recruitment].ycs_values{2008} 0.000 0.000 0.503 0.503 0.503 0.000 0.000 0.503
process[Recruitment].ycs_values{2009} 0.000 0.000 1.010 1.010 1.010 0.000 0.000 1.010
process[Recruitment].ycs_values{2010} 0.000 0.000 0.674 0.675 0.675 0.000 0.000 0.674
process[Recruitment].ycs_values{2011} 0.000 0.000 1.004 1.004 1.004 0.000 0.000 1.004
process[Recruitment].ycs_values{2012} 0.000 0.000 -0.311 -0.311 -0.311 0.000 0.000 -0.311
process[Recruitment].ycs_values{2013} 0.000 0.000 1.918 1.919 1.919 0.000 0.000 1.918
process[Recruitment].ycs_values{2014} 0.000 0.000 0.262 0.265 0.265 0.000 0.000 0.262

CASAL objective function component values
Component Base_Model Sensitivity_1
Tangaroa_bio_autumn -6.829 -6.834
Tangaroa_bio_summer -23.884 -23.962
Tangaroa_propn_at_age_aut 175.718 175.789
Tangaroa_propn_at_age_summer 835.903 835.602
longline_Campbell_home_propn_at_age 275.676 275.416
longline_Puysegur_spawn_propn_at_age 363.279 363.252
trawl_observer_propn_at_age 682.612 682.293
prior_on_q[tan_sum].q -2.364 -2.366
prior_on_q[tan_aut].q -2.033 -2.037
prior_on_initialization.B0 12.641 12.646
prior_on_natural_mortality.ogive_all 0.000 0.000
prior_on_selectivity[surveysum_sel].male 0.000 0.000
prior_on_selectivity[surveysum_sel].female 0.000 0.000
prior_on_selectivity[surveyaut_sel].male 0.000 0.000
prior_on_selectivity[surveyaut_sel].female 0.000 0.000
prior_on_selectivity[trawl_sel].male 0.000 0.000
prior_on_selectivity[trawl_sel].female 0.000 0.000
prior_on_selectivity[line_home_sel].male 0.000 0.000
prior_on_selectivity[line_home_sel].female 0.000 0.000
prior_on_selectivity[line_spawn_sel].male 0.000 0.000
prior_on_selectivity[line_spawn_sel].female 0.000 0.000
prior_on_recruitment.YCS -14.441 -14.366
clp1 0.000 0.000
clp2 0.000 0.000
clp3 0.000 0.000
YCS_average_1 0.908 0.903
Total 2297.190 2296.340
Casal2 objective function component values
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992                  -1.693 -1.693 -1.679 -1.679 -1.679 -1.693 -1.693 -1.679
observation->summerTANbiomass-1993                  -1.353 -1.353 -1.331 -1.331 -1.331 -1.353 -1.353 -1.331
observation->summerTANbiomass-1994                  -0.975 -0.975 -0.991 -0.991 -0.991 -0.975 -0.975 -0.991
observation->summerTANbiomass-2001                  0.430 0.430 0.354 0.354 0.354 0.430 0.430 0.354
observation->summerTANbiomass-2002                  -1.778 -1.778 -1.786 -1.786 -1.786 -1.778 -1.778 -1.786
observation->summerTANbiomass-2003                  -1.685 -1.685 -1.693 -1.693 -1.693 -1.685 -1.685 -1.693
observation->summerTANbiomass-2004                  -1.598 -1.598 -1.586 -1.586 -1.586 -1.598 -1.598 -1.586
observation->summerTANbiomass-2005                  -1.657 -1.657 -1.656 -1.656 -1.656 -1.657 -1.657 -1.656
observation->summerTANbiomass-2006                  -1.143 -1.143 -1.153 -1.153 -1.153 -1.143 -1.143 -1.153
observation->summerTANbiomass-2007                  -1.162 -1.162 -1.180 -1.180 -1.180 -1.162 -1.162 -1.180
observation->summerTANbiomass-2008                  -1.568 -1.568 -1.553 -1.553 -1.553 -1.568 -1.568 -1.553
observation->summerTANbiomass-2009                  -1.700 -1.700 -1.705 -1.705 -1.705 -1.700 -1.700 -1.705
observation->summerTANbiomass-2010                  -1.672 -1.672 -1.678 -1.678 -1.678 -1.672 -1.672 -1.678
observation->summerTANbiomass-2012                  -1.554 -1.554 -1.558 -1.558 -1.558 -1.554 -1.554 -1.558
observation->summerTANbiomass-2013                  -1.669 -1.669 -1.667 -1.667 -1.667 -1.669 -1.669 -1.667
observation->summerTANbiomass-2015                  -1.582 -1.582 -1.570 -1.570 -1.570 -1.582 -1.582 -1.570
observation->summerTANbiomass-2017                  -1.526 -1.526 -1.528 -1.528 -1.528 -1.526 -1.526 -1.528
observation->Tangaroa_propn_at_age_summer-1990                  44.218 44.218 44.393 44.393 44.393 44.218 44.218 44.393
observation->Tangaroa_propn_at_age_summer-1992                  51.993 51.993 51.753 51.753 51.753 51.993 51.993 51.753
observation->Tangaroa_propn_at_age_summer-1993                  50.200 50.200 50.168 50.168 50.168 50.200 50.200 50.168
observation->Tangaroa_propn_at_age_summer-1994                  49.743 49.743 49.785 49.785 49.785 49.743 49.743 49.785
observation->Tangaroa_propn_at_age_summer-2001                  48.355 48.355 48.237 48.237 48.237 48.355 48.355 48.237
observation->Tangaroa_propn_at_age_summer-2002                  47.830 47.830 47.879 47.879 47.879 47.830 47.830 47.879
observation->Tangaroa_propn_at_age_summer-2003                  48.442 48.442 48.620 48.620 48.620 48.442 48.442 48.620
observation->Tangaroa_propn_at_age_summer-2004                  44.823 44.823 44.865 44.865 44.865 44.823 44.823 44.865
observation->Tangaroa_propn_at_age_summer-2005                  43.097 43.097 43.117 43.117 43.117 43.097 43.097 43.117
observation->Tangaroa_propn_at_age_summer-2006                  43.891 43.891 44.058 44.058 44.058 43.891 43.891 44.058
observation->Tangaroa_propn_at_age_summer-2007                  41.848 41.848 41.841 41.841 41.841 41.848 41.848 41.841
observation->Tangaroa_propn_at_age_summer-2008                  45.225 45.225 45.267 45.267 45.267 45.225 45.225 45.267
observation->Tangaroa_propn_at_age_summer-2009                  46.844 46.844 46.806 46.806 46.806 46.844 46.844 46.806
observation->Tangaroa_propn_at_age_summer-2010                  47.128 47.128 47.202 47.202 47.202 47.128 47.128 47.202
observation->Tangaroa_propn_at_age_summer-2012                  44.353 44.353 44.183 44.183 44.183 44.353 44.353 44.183
observation->Tangaroa_propn_at_age_summer-2013                  47.251 47.251 47.021 47.021 47.021 47.251 47.251 47.021
observation->Tangaroa_propn_at_age_summer-2015                  46.473 46.473 46.342 46.342 46.342 46.473 46.473 46.342
observation->Tangaroa_propn_at_age_summer-2017                  44.182 44.182 44.082 44.082 44.082 44.182 44.182 44.082
observation->autumnTANbiomass-1992                  -1.558 -1.558 -1.572 -1.572 -1.572 -1.558 -1.558 -1.572
observation->autumnTANbiomass-1993                  -1.741 -1.741 -1.733 -1.733 -1.733 -1.741 -1.741 -1.733
observation->autumnTANbiomass-1996                  -1.779 -1.779 -1.779 -1.779 -1.779 -1.779 -1.779 -1.779
observation->autumnTANbiomass-1998                  -1.750 -1.750 -1.750 -1.750 -1.750 -1.750 -1.750 -1.750
observation->Tangaroa_propn_at_age_autumn-1992                  44.589 44.589 44.443 44.443 44.443 44.589 44.589 44.443
observation->Tangaroa_propn_at_age_autumn-1993                  45.484 45.484 45.443 45.443 45.443 45.484 45.484 45.443
observation->Tangaroa_propn_at_age_autumn-1996                  42.184 42.184 42.295 42.295 42.295 42.184 42.184 42.295
observation->Tangaroa_propn_at_age_autumn-1998                  43.464 43.464 43.610 43.610 43.610 43.464 43.464 43.610
observation->trawl_propn_at_age-1992                  36.067 36.067 35.944 35.944 35.944 36.067 36.067 35.944
observation->trawl_propn_at_age-1993                  27.516 27.516 27.476 27.476 27.476 27.516 27.516 27.476
observation->trawl_propn_at_age-1994                  25.819 25.819 25.764 25.764 25.764 25.819 25.819 25.764
observation->trawl_propn_at_age-1996                  28.394 28.394 28.397 28.397 28.397 28.394 28.394 28.397
observation->trawl_propn_at_age-1998                  24.915 24.915 24.910 24.910 24.910 24.915 24.915 24.910
observation->trawl_propn_at_age-2001                  24.580 24.580 24.542 24.542 24.542 24.580 24.580 24.542
observation->trawl_propn_at_age-2002                  26.770 26.770 26.792 26.792 26.792 26.770 26.770 26.792
observation->trawl_propn_at_age-2003                  34.564 34.564 34.511 34.511 34.511 34.564 34.564 34.511
observation->trawl_propn_at_age-2004                  29.608 29.608 29.608 29.608 29.608 29.608 29.608 29.608
observation->trawl_propn_at_age-2005                  30.147 30.147 30.166 30.166 30.166 30.147 30.147 30.166
observation->trawl_propn_at_age-2006                  33.629 33.629 33.714 33.714 33.714 33.629 33.629 33.714
observation->trawl_propn_at_age-2007                  26.635 26.635 26.588 26.588 26.588 26.635 26.635 26.588
observation->trawl_propn_at_age-2008                  27.059 27.059 27.076 27.076 27.076 27.059 27.059 27.076
observation->trawl_propn_at_age-2009                  37.213 37.213 37.237 37.237 37.237 37.213 37.213 37.237
observation->trawl_propn_at_age-2010                  30.648 30.648 30.694 30.694 30.694 30.648 30.648 30.694
observation->trawl_propn_at_age-2011                  31.266 31.266 31.260 31.260 31.260 31.266 31.266 31.260
observation->trawl_propn_at_age-2012                  32.325 32.325 32.366 32.366 32.366 32.325 32.325 32.366
observation->trawl_propn_at_age-2013                  37.072 37.072 36.943 36.943 36.943 37.072 37.072 36.943
observation->trawl_propn_at_age-2014                  30.640 30.640 30.642 30.642 30.642 30.640 30.640 30.642
observation->trawl_propn_at_age-2015                  33.456 33.456 33.474 33.474 33.474 33.456 33.456 33.474
observation->trawl_propn_at_age-2016                  36.532 36.532 36.482 36.482 36.482 36.532 36.532 36.482
observation->trawl_propn_at_age-2017                  37.755 37.755 37.708 37.708 37.708 37.755 37.755 37.708
observation->longline_Campbell_home_propn_at_age-1999                  45.348 45.348 45.256 45.256 45.256 45.348 45.348 45.256
observation->longline_Campbell_home_propn_at_age-2001                  31.965 31.965 31.950 31.950 31.950 31.965 31.965 31.950
observation->longline_Campbell_home_propn_at_age-2003                  28.644 28.644 28.675 28.675 28.675 28.644 28.644 28.675
observation->longline_Campbell_home_propn_at_age-2005                  32.750 32.750 32.776 32.776 32.776 32.750 32.750 32.776
observation->longline_Campbell_home_propn_at_age-2009                  26.033 26.033 25.611 25.611 25.611 26.033 26.033 25.611
observation->longline_Campbell_home_propn_at_age-2010                  24.302 24.302 24.461 24.461 24.461 24.302 24.302 24.461
observation->longline_Campbell_home_propn_at_age-2011                  28.878 28.878 28.935 28.935 28.935 28.878 28.878 28.935
observation->longline_Campbell_home_propn_at_age-2012                  32.258 32.258 32.389 32.389 32.389 32.258 32.258 32.389
observation->longline_Campbell_home_propn_at_age-2014                  25.495 25.495 25.357 25.357 25.357 25.495 25.495 25.357
observation->longline_Puyseger_home_propn_at_age-2000                  42.745 42.745 42.680 42.680 42.680 42.745 42.745 42.680
observation->longline_Puyseger_home_propn_at_age-2001                  31.770 31.770 31.900 31.900 31.900 31.770 31.770 31.900
observation->longline_Puyseger_home_propn_at_age-2002                  39.978 39.978 39.998 39.998 39.998 39.978 39.978 39.998
observation->longline_Puyseger_home_propn_at_age-2003                  43.527 43.527 43.511 43.511 43.511 43.527 43.527 43.511
observation->longline_Puyseger_home_propn_at_age-2004                  39.957 39.957 40.015 40.015 40.015 39.957 39.957 40.015
observation->longline_Puyseger_home_propn_at_age-2005                  25.532 25.532 25.358 25.358 25.358 25.532 25.532 25.358
observation->longline_Puyseger_home_propn_at_age-2006                  35.210 35.210 35.426 35.426 35.426 35.210 35.210 35.426
observation->longline_Puyseger_home_propn_at_age-2007                  33.981 33.981 33.782 33.782 33.782 33.981 33.981 33.782
observation->longline_Puyseger_home_propn_at_age-2008                  19.139 19.139 19.113 19.113 19.113 19.139 19.139 19.113
observation->longline_Puyseger_home_propn_at_age-2010                  24.238 24.238 24.366 24.366 24.366 24.238 24.238 24.366
observation->longline_Puyseger_home_propn_at_age-2017                  27.200 27.200 27.093 27.093 27.093 27.200 27.200 27.093
prior->B0->process[Recruitment].b0               12.640 12.640 12.646 12.646 12.646 12.640 12.640 12.646
prior->summerTANq->catchability[summerTANq].q                -2.363 -2.363 -2.365 -2.365 -2.365 -2.363 -2.363 -2.365
prior->autumnTANq->catchability[autumnTANq].q                -2.035 -2.035 -2.037 -2.037 -2.037 -2.035 -2.035 -2.037
prior->M_all_x0->selectivity[M_all].x0               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y0->selectivity[M_all].y0               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y1->selectivity[M_all].y1               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y2->selectivity[M_all].y2               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].mu               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].sigma_l          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].sigma_r          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].mu               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].sigma_l          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].sigma_r          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->process[Recruitment].ycs_values{1972} -0.378 -0.378 -0.365 -0.365 -0.365 -0.378 -0.378 -0.365
prior->process[Recruitment].ycs_values{1973} -0.360 -0.360 -0.349 -0.349 -0.349 -0.360 -0.360 -0.349
prior->process[Recruitment].ycs_values{1974} -0.397 -0.397 -0.398 -0.398 -0.398 -0.397 -0.397 -0.398
prior->process[Recruitment].ycs_values{1975} -0.398 -0.398 -0.398 -0.398 -0.398 -0.398 -0.398 -0.398
prior->process[Recruitment].ycs_values{1976} -0.380 -0.380 -0.383 -0.383 -0.383 -0.380 -0.380 -0.383
prior->process[Recruitment].ycs_values{1977} -0.399 -0.399 -0.398 -0.398 -0.398 -0.399 -0.399 -0.398
prior->process[Recruitment].ycs_values{1978} -0.398 -0.398 -0.396 -0.396 -0.396 -0.398 -0.398 -0.396
prior->process[Recruitment].ycs_values{1979} -0.335 -0.335 -0.316 -0.316 -0.316 -0.335 -0.335 -0.316
prior->process[Recruitment].ycs_values{1980} -0.380 -0.380 -0.372 -0.372 -0.372 -0.380 -0.380 -0.372
prior->process[Recruitment].ycs_values{1981} -0.231 -0.231 -0.213 -0.213 -0.213 -0.231 -0.231 -0.213
prior->process[Recruitment].ycs_values{1982} -0.364 -0.364 -0.367 -0.367 -0.367 -0.364 -0.364 -0.367
prior->process[Recruitment].ycs_values{1983} -0.326 -0.326 -0.319 -0.319 -0.319 -0.326 -0.326 -0.319
prior->process[Recruitment].ycs_values{1984} -0.291 -0.291 -0.292 -0.292 -0.292 -0.291 -0.291 -0.292
prior->process[Recruitment].ycs_values{1985} -0.394 -0.394 -0.393 -0.393 -0.393 -0.394 -0.394 -0.393
prior->process[Recruitment].ycs_values{1986} -0.114 -0.114 -0.117 -0.117 -0.117 -0.114 -0.114 -0.117
prior->process[Recruitment].ycs_values{1987} -0.135 -0.135 -0.134 -0.134 -0.134 -0.135 -0.135 -0.134
prior->process[Recruitment].ycs_values{1988} -0.334 -0.334 -0.334 -0.334 -0.334 -0.334 -0.334 -0.334
prior->process[Recruitment].ycs_values{1989} -0.375 -0.375 -0.372 -0.372 -0.372 -0.375 -0.375 -0.372
prior->process[Recruitment].ycs_values{1990} -0.350 -0.350 -0.350 -0.350 -0.350 -0.350 -0.350 -0.350
prior->process[Recruitment].ycs_values{1991} -0.384 -0.384 -0.385 -0.385 -0.385 -0.384 -0.384 -0.385
prior->process[Recruitment].ycs_values{1992} -0.367 -0.367 -0.369 -0.369 -0.369 -0.367 -0.367 -0.369
prior->process[Recruitment].ycs_values{1993} -0.225 -0.225 -0.217 -0.217 -0.217 -0.225 -0.225 -0.217
prior->process[Recruitment].ycs_values{1994} -0.233 -0.233 -0.232 -0.232 -0.232 -0.233 -0.233 -0.232
prior->process[Recruitment].ycs_values{1995} -0.192 -0.192 -0.185 -0.185 -0.185 -0.192 -0.192 -0.185
prior->process[Recruitment].ycs_values{1996} -0.319 -0.319 -0.315 -0.315 -0.315 -0.319 -0.319 -0.315
prior->process[Recruitment].ycs_values{1997} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{1998} -0.372 -0.372 -0.373 -0.373 -0.373 -0.372 -0.372 -0.373
prior->process[Recruitment].ycs_values{1999} -0.360 -0.360 -0.360 -0.360 -0.360 -0.360 -0.360 -0.360
prior->process[Recruitment].ycs_values{2000} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2001} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2002} -0.378 -0.378 -0.377 -0.377 -0.377 -0.378 -0.378 -0.377
prior->process[Recruitment].ycs_values{2003} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2004} -0.383 -0.383 -0.383 -0.383 -0.383 -0.383 -0.383 -0.383
prior->process[Recruitment].ycs_values{2005} -0.249 -0.249 -0.251 -0.251 -0.251 -0.249 -0.249 -0.251
prior->process[Recruitment].ycs_values{2006} -0.375 -0.375 -0.375 -0.375 -0.375 -0.375 -0.375 -0.375
prior->process[Recruitment].ycs_values{2007} -0.252 -0.252 -0.253 -0.253 -0.253 -0.252 -0.252 -0.253
prior->process[Recruitment].ycs_values{2008} -0.368 -0.368 -0.370 -0.370 -0.370 -0.368 -0.368 -0.370
prior->process[Recruitment].ycs_values{2009} -0.320 -0.320 -0.326 -0.326 -0.326 -0.320 -0.320 -0.326
prior->process[Recruitment].ycs_values{2010} -0.362 -0.362 -0.364 -0.364 -0.364 -0.362 -0.362 -0.364
prior->process[Recruitment].ycs_values{2011} -0.392 -0.392 -0.390 -0.390 -0.390 -0.392 -0.392 -0.390
prior->process[Recruitment].ycs_values{2012} -0.394 -0.394 -0.393 -0.393 -0.393 -0.394 -0.394 -0.393
prior->process[Recruitment].ycs_values{2013} -0.389 -0.389 -0.393 -0.393 -0.393 -0.389 -0.389 -0.393
prior->process[Recruitment].ycs_values{2014} -0.396 -0.396 -0.396 -0.396 -0.396 -0.396 -0.396 -0.396
additional_prior->YCS_average_1                  0.908 0.908 0.904 0.904 0.904 0.908 0.908 0.904
total_score                  2296.970 2296.970 2296.140 2296.140 2296.140 2296.970 2296.970 2296.140

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-06"                                                                   
## [2] "fmm: have converged: t = 9.43571e-07 f = 2296.34"                                                         
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 197 quasi-Newton iterations using 312 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)
## [1] "CASAL base model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.735942 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.986887 0.996747"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"